Re: [ccp4bb] Another folding AI

2022-11-06 Thread Carter, Charlie 
Colin,

A former graduate student of mine alerted me to Box GEP, Hunter WG, Hunter JS. 
1978. Statistics for Experimenters. New York: Wiley Interscience in ~1984. I 
bought a new copy then and have very likely spent more time inside that book 
than any other over the years since then. So I’m entirely in your court about 
Box’s contributions.

On the other hand, as I diverged from crystallography into mechanistic 
enzymology and other areas, I began to realize that comments such as those you 
cited also have had the adverse affect of persuading people not to build models 
at all and even to induce real skepticism about building and testing models. I 
find that a shame.

Charlie

On Nov 6, 2022, at 3:12 PM, Nave, Colin (DLSLtd,RAL,LSCI) 
<64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk>
 wrote:

You don't often get email from 
64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is important
All these quotes are great fun and worth keeping in mind, along with many 
others. I hadn’t realised that the creationists had adopted James Clark Maxwell 
as one of their own. However he didn’t go as far as one present day scientist 
who believes the earth is no more than 10,000 years old. Which discipline? 
Palaeontology of course. This person is not even some old fossil.

I always liked George Box’s comments about models. I remember Eleanor Dodson 
saying, probably at some CCP4 refinement study weekend, that a structure 
obtained by protein crystallography was like a curate’s egg. She might have 
predated George Box with this thought.

There should not  be any doubt that AF2 models are useful though. The question 
is how far their usefulness extends.


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Bryan Lepore
Sent: 05 November 2022 17:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another folding AI

And of course,

"... all models are approximations. Essentially, all models are wrong, but some 
are useful. However, the approximate nature of the model must always be borne 
in mind"

Box, G. E. P.; Draper, N. R. (1987)
Empirical Model-Building and Response Surfaces
John Wiley & Sons

"Since all models are wrong the scientist must be alert to what is importantly 
wrong. It is inappropriate to be concerned about mice when there are tigers 
abroad."

Box, George E. P. (1976)
"Science and 
statistics"
Journal of the American Statistical 
Association
71 (356): 791-799
doi:10.1080/01621459.1976.10480949

https://en.m.wikipedia.org/wiki/All_models_are_wrong



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Re: [ccp4bb] Another folding AI

2022-11-06 Thread Ian Tickle 
Hi Colin

That seems to be a fundamental misinterpretation of what Maxwell actually
said (and being half Scot myself I feel obliged to defend him!).  To add
one more quote to the mix, that of Charles Petzold in his review of the
historical evidence for the claim of the creationists:

*Abstract:* Modern-day Christian creationists have claimed
nineteenth-century Scottish physicist James Clerk Maxwell as one of their
own. The author explores the historical evidence and discovers that
Maxwell's attitude toward evolution was more nuanced than people assume.
The characterization of Maxwell as an anti-Darwin creationist is based on
exaggerations, misinterpretations, and (probably most of all) wishful
thinking.

https://www.charlespetzold.com/etc/MaxwellMoleculesAndEvolution.html

Cheers

-- Ian


On Sun, 6 Nov 2022 at 20:13, Nave, Colin (DLSLtd,RAL,LSCI) <
64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk> wrote:

> All these quotes are great fun and worth keeping in mind, along with many
> others. I hadn’t realised that the creationists had adopted James Clark
> Maxwell as one of their own. However he didn’t go as far as one present day
> scientist who believes the earth is no more than 10,000 years old. Which
> discipline? Palaeontology of course. This person is not even some old
> fossil.
>
>
>
> I always liked George Box’s comments about models. I remember Eleanor
> Dodson saying, probably at some CCP4 refinement study weekend, that a
> structure obtained by protein crystallography was like a curate’s egg. She
> might have predated George Box with this thought.
>
>
>
> There should not  be any doubt that AF2 models are useful though. The
> question is how far their usefulness extends.
>
>
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Bryan
> Lepore
> *Sent:* 05 November 2022 17:03
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Another folding AI
>
>
>
> And of course,
>
>
>
> "... all models are approximations. Essentially, all models are wrong, but
> some are useful. However, the approximate nature of the model must always
> be borne in mind"
>
>
>
> Box, G. E. P.; Draper, N. R. (1987)
>
> Empirical Model-Building and Response Surfaces
>
> John Wiley & Sons
>
>
>
> "Since all models are wrong the scientist must be alert to what is
> importantly wrong. It is inappropriate to be concerned about mice when
> there are tigers abroad."
>
>
>
> Box, George E. P. (1976)
>
> "Science and statistics"
> 
>
> Journal of the American Statistical Association
> 
>
> *71* (356): 791-799
>
> doi :
> 10.1080/01621459.1976.10480949
> 
>
>
>
> https://en.m.wikipedia.org/wiki/All_models_are_wrong
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
>
> --
>
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
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>
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Re: [ccp4bb] Another folding AI

2022-11-06 Thread Nave, Colin (DLSLtd,RAL,LSCI) 
All these quotes are great fun and worth keeping in mind, along with many 
others. I hadn’t realised that the creationists had adopted James Clark Maxwell 
as one of their own. However he didn’t go as far as one present day scientist 
who believes the earth is no more than 10,000 years old. Which discipline? 
Palaeontology of course. This person is not even some old fossil.

I always liked George Box’s comments about models. I remember Eleanor Dodson 
saying, probably at some CCP4 refinement study weekend, that a structure 
obtained by protein crystallography was like a curate’s egg. She might have 
predated George Box with this thought.

There should not  be any doubt that AF2 models are useful though. The question 
is how far their usefulness extends.


From: CCP4 bulletin board  On Behalf Of Bryan Lepore
Sent: 05 November 2022 17:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another folding AI


And of course,



"... all models are approximations. Essentially, all models are wrong, but some 
are useful. However, the approximate nature of the model must always be borne 
in mind"



Box, G. E. P.; Draper, N. R. (1987)

Empirical Model-Building and Response Surfaces

John Wiley & Sons



"Since all models are wrong the scientist must be alert to what is importantly 
wrong. It is inappropriate to be concerned about mice when there are tigers 
abroad."



Box, George E. P. (1976)

"Science and 
statistics"

Journal of the American Statistical 
Association

71 (356): 791-799

doi:10.1080/01621459.1976.10480949



https://en.m.wikipedia.org/wiki/All_models_are_wrong



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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This e-mail and any attachments may contain confidential, copyright and or 
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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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